2016-12-14 introduction to gbif. gbif seminar in bergen
TRANSCRIPT
GBIFenablesfreeandopenaccesstobiodiversitydataonline.
Weareaninterna:onalgovernment-ini:atedand-fundedini:a:vefocusedonmakingbiodiversitydataavailabletoallandanyone,forscien:ficresearch,conserva:onandsustainabledevelopment.
Status9thDecember2016
GBIFprovidesaninfrastructuretodiscoverdata
globalregistry dataportal
thatisdependentonresolvableandstableiden<fiersforfullfunc<onality
Research institute
Biodiversity ConservationBiodiversity
AnalysisGBIF portal
Global information systems
Scientific Research
STANDARD MULTIPLE-PURPOSE DATA-SERVICES
Data integration & data interoperability
GEOBONBiodiversityobserva:onnetwork
INTERGOVERNMENTAL GROUP ON EARTH OBSERVATIONS
MAP OF NATIONAL PARTICIPANTS
Updated November 2016
parti
cipa
tion
Asia (lack of data)
Africa (lack of data)
DATA PUBLISHED BY COUNTRY, YTD 2016 AS OF 31 OCT 2016
All others
NZAU
DK
ES
CO
NO
ZADE
NL
US
1 United States 14,258,959 2 Netherlands 12,707,525 3 Germany 11,636,441 4 South Africa 9,303,521 5 Norway 4,257,569 6 Colombia 3,725,644 7 Spain 3,161,768 8 Denmark 3,032,962 9 Australia 2,070,365
10 New Zealand 1,844,320
NOTE: Datasets are assigned to countries according to the location of the publishing institution, including aggregated datasets with contributors from many other countries
data
ava
ilabi
lity
TOTAL DATA PUBLISHED BY COUNTRY AS OF 31 OCT 2016
All others
BE
ES
ZA
GB
NL
DE
AU
FRSE
US
1 United States 269,908,182 2 Sweden 53,791,605 3 France 39,900,258 4 Australia 37,232,140 5 Germany 27,003,112 6 Netherlands 25,709,366 7 United Kingdom 22,986,875 8 Norway 22,534,127 9 South Africa 20,441,422
10 Spain 14,474,227
data
ava
ilabi
lity
DATA DOWNLOAD REQUESTS BY COUNTRY, YTD 2016 AS OF 31 OCT 2016
All others
IT
CN
IN
ZA
GBCO
ES
BR
MX
US
1 United States 12,305 2 Mexico 11,982 3 Brazil 6,769 4 Spain 4,511 5 Colombia 4,470 6 United Kingdom 4,257 7 South Africa 2,938 8 India 2,902 9 China 2,724
10 Italy 2,007
Users of occurrence data in Norway generally use Artskart.
data
acc
ess
and
use
2016
2015
2014
2013
2012
2011
2010
2009
2008
0 125 250 375 500
416
52
89
148
169
229
249
350
407
347
Peer-reviewed publications using GBIF-mediated data 2016 projection
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DAT
A A
CC
ESS
AN
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SE
Peer-reviewed publications using GBIF-mediated data
PEER-REVIEWED USES, BY COUNTRY AND REGION, 2016 AS OF 31 OCT 2016
Oceania
North America
Latin AmericaEurope
Asia
Africa
�1
Year-to-date 2016
1 United States 126
2 Brazil 45
3 United Kingdom 42
4 Germany 40
5 Australia 39
6 China 37
7 Mexico 33
8 France 32
9 Spain 21
10 Canada 20
October 2016 1 United States 15 2 Brazil 8 3 Mexico 6 3 United Kingdom 6 5 Australia 4 6 Denmark 3 6 Germany 3 6 Netherlands 3
data
acc
ess
and
use
2016
Norwayyear-to-date2016,19publica<ons
RESEARCH EXAMPLES NORWAY YTD 2016
Araújo R, Assis J, Aguillar R, Airoldi L, Bárbara I, Bartsch I, Bekkby T et al. (2016) Status, trends and drivers of kelp forests in Europe: an expert assessment. Biodiversity and Conservation 25(7) 1319-1348. DOI:10.1007/s10531-016-1141-7.
Gjershaug JO, Frode Ødegaard F, Staverløkk A & Olsen KM (2016) Records of bilateral gynandromorphism in three species of ants (Hymenoptera, Formicidae) in Norway. Norwegian Journal of Entomology 63(1): 65-70.
Phillips J, Asdal Å, Brehm JM, Rasmussen M, Maxted N (2016) In situ and ex situ diversity analysis of priority crop wild relatives in Norway. Diversity and distributions 22(11): 1112-1126. DOI: 10.1111/ddi.12470
Özkan Ş, Andrea Vitali, Nicola Lacetera, Barbara Amon, André Bannink, Dave J. Bartley, et al. (2016) Challenges and priorities for modelling livestock health and pathogens in the context of climate change. Environmental Research 151: 130-144. DOI: 10.1016/j.envres.2016.07.033
Bjerke JW, Bokhorst S, Callaghan TV, Phoenix GK (2016) Persistent reduction of segment growth and photosynthesis in a widespread and important sub-Arctic moss species after cessation of three years of experimental winter warming. Functional Ecology. DOI: 10.1111/1365-2435.12703
Wauchope HS, Shaw JD, Varpe Ø, Lappo EG, Boertmann D, & Lanctot RB (2016) Rapid climate-driven loss of breeding habitat for Arctic migratory birds. Global Change Biology. DOI: 10.1111/gcb.13404
Norway year-to-date, 19 publications https://www.mendeley.com/groups/1068301/gbif-public-library/papers/added/0/tag/Norway/
data
acc
ess
and
use
2016 SCIENCE REVIEW
Just published! Annual publication summarizes more than 100 peer-reviewed articles that rely on GBIF-mediated data. Accompanying Sourcebook includes more than 400 citations. Download: § gbif.org/science-review § gbif.org/science-review-sourcebook-2016
http://www.gbif.org/science-review
dat
a ac
cess
and
use
LATEST NEWS
First BID grants provide nearly €1 million in funding to 23 African projects ¤ EU-funded programme grantees
represent 34 organizations from 20 African countries (Read more)
¤ Open call for Caribbean and the Pacific (read more)
¤ Read more about BID
http://www.gbif.org/newsroom/summary Photos: (left) One Tree Plain, CC BY-NC-SA 2015 Geoff Livingston, (centre) Peacock pansy (Junonia almana), Ho Chi Minh, Vietnam.
CC BY-SA 2015 Pavel Kirillov via iNaturalist. (right) Photo courtesy of Nestor Engone Obiang.
com
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ns
BIFA grants to benefit 14 Asian countries Four project share €106,000 in funding to enhance data publishing capacity of current and future network members. Read more
Belgium, Taiwan and Norway nodes provided BIFA funded mentoring for the AESEAN heritage parks in July 2017. Read more (at gbif.no)
Appeal for help after damage Gabon's national herbarium
Post-election riots in September spared collections, but caused major damage to the BID grantee’s headquarters in Libreville, Gabon.
Read English or French
LATEST NEWS
Four network projects awarded 2016 capacity enhancement support grants (mentoring) ¤ A total of €23,300 in funding will
support the work of GBIF nodes and partners in five countries (Colombia, France, Guinea, Portugal, Spain).
¤ Read more
http://www.gbif.org/newsroom/summary Photos:. (center) courtesy of GBIF Portugal.
(right) Red-crested pochards (Netta rufina) off the eastern shore of Obersee, Switzerland, photo by roby 2016 CC BY-NC via iNaturalist.
com
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icatio
ns
Four countries become the GBIF network’s newest national members ¤ Switzerland (voting) ¤ Ecuador (associate) ¤ Niger (associate) ¤ Nigeria (associate)
New Darwin Core templates released Pre-configured Excel templates simplify data formatting, preparation and publication. – metadata template – checklist template – occurrence template – sampling event template Read more Template tool from GBIF.no
LATEST NEWS
http://www.gbif.org/newsroom/summary Photos: (far right) © 2016 Williams Fagner.
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ns
Data licensing milestone
All species occurrence datasets on GBIF.org now carry standardized Creative Commons licenses.
CC0 57 % CC-BY 4.0 31 % CC-BY-NC 4.0 13 %
Read initial announcement and update
2016 Ebbe Nielsen Challenge winner
Alejandro Ruete (Argentina, postdoc at SLU, Sweden) seeks to calculate ‘Where and when is there enough data?’
Read more
2016 Young Researchers Awards
Meet the winners!
– Mexican PhD student Juan M. Escamilla Mólgora
– Brazilian Master’s student Bruno Umbelino
PUBLISH DATA IN GBIF da
ta p
ublis
hing
Step 1: data holding research institutes seek endorsement as an approved data publisher.
Step 2: datasets are identified and converted to standard Darwin Core format.
Step 3: datasets can be published directly from the data node and/or with the assistance from a national (or thematic) GBIF node.
Some (citizen science) data platforms publish in GBIF.
GBIF DATA PORTAL API An interface to access data published through the GBIF network using web services.
ROPENSCI : RGBIF library(rgbif) key <- name_backbone(name='Hepatica nobilis', kingdom=‘Plantae')$speciesKey sp <- occ_search(taxonKey=key, return='data', hasCoordinate=TRUE, limit=1000) gbifmap(sp)
GBIFportal:
22,9millionoccurrenceswithloca:onsinNorway.Publishedfrom31countriesworldwide.
Updated9thDecember2016
Finland
Norway Sweden
Iceland
Nov2016 Datasets Occurrences
Denmark 68+1 11919745Finland 54 3164965Iceland 4 458705Norway 117+2+5 22558484Sweden 42 53818302
h\p://www.gbif.o
rg/cou
ntry/N
O
STATUS FOR NORDIC GBIF NODES (DATA HOSTED BY…)
Danmark
NodeteamatNHM,UniversityofOsloDagEndresen,NodemanagerChris:anSvindseth,Databasemanager
FridtjofMehlum,ResearchdirectorEinarTimdal,AssociateprofessorGeirSøli,AssociateprofessorVidarBakken,Consultant
Artsdatabanken,Trondheim
WouterKochNilsValland
NTNUUniversityMuseumAndersFinstad,GBIFSciencecommiLee
ResearchCouncilofNorway
PerBacke-Hansen,Headofdelega<on
Contactusat:[email protected]